How to Build CHD@ZJU

CHD related Articles were retrieved from Pubmed, by entering keywords "coronary heart disease" and constrict the publish date from 2000/1/1 to now (2013/1/23). As a result, totally 115898 articles were found and their abstracts were downloaded for text mining. Since some articles didn't contain abstracts, only 88396 abstracts remained.

The text-mining process to get CHD related genes could be divided in to 5 following steps:

  • 1) Extracting all keywords from abstracts and ignoring those keywords start with numbers. 101402 keywords were extracted.

  • 2) Input these keywords into Gene library in ArrayTrack and find possible related genes. 4674 genes were then found.

  • 3) Put these 4674 genes again into pubmed abstracts to find related aticles. Only genes which offical name or there keyword description (such as prolactin for gene PRL) could be found in the abstract would be remained. As a result, 1247 genes were remained.

  • 4) Manually examined on the 1247 genes to validate it was acutally related to CHD. Some genes would be filtered if it represents other meanings (such as gene CAD, Entrez ID:790, carbamoyl-phosphate synthetase 2, is mostly meant coronary arterial disease in articles). 681 genes were then validated with at least one reference.

  • 5) All genes was compared with 1078 CHD genes in RGD database, and 370 genes were overlapped. These 370 genes were labels as "RGD_Supported" and the other 293 genes were labels as "REFERED". All 663 genes had supported references in CHD@ZJU which were examined by step 4.
  • How To contact Us

    Collaboration Information: Prof. Xiaohui Fan (fanxh@zju.edu.cn)

    Website using assistance : Leihong Wu (11019004@zju.edu.cn)



    Basic Information

    Gene Name: FGFR4

    Description: fibroblast growth factor receptor 4

    Entrez Gene ID: 2264

    SwissProt Acc Number: P22455

    RefSeq: NM_002011

    It was supported literatures to be a novel CHD related gene:

    ..Our data suggested that the FGFR4 rs351855G/A (Gly388Arg) and rs147603016G/A polymorphisms could act as protective factors against CAD in the Chinese population and indicated that a single gene polymorphism could have diverse functions in different diseases...

    From PMID: 22696188, in Journal Mol Biol Rep. , 2012


    References

    There were 4 potential papers with FGFR4 and CHD.

    PMIDTitleJournalsDetails
    21945708 Expression of FGF23/KLOTHO system in human vascular tissue.International journal of cardiologyMore Details
    22696188 Fibroblast growth factor receptor 4 polymorphisms and coronary artery disease: a case control study.Molecular biology reportsMore Details
    22313031 Fibroblast growth factor receptor 4 polymorphisms and susceptibility to coronary artery disease.DNA and cell biologyMore Details
    22587598 Fibroblast growth factor receptor 4 polymorphisms are associated with coronary artery disease.Genetic testing and molecular biomarkersMore Details

    NOTEs: These result is mostly from TEXT-MINING and there might have mismatches.



    PPI interactions

    There were totally 20 unique genes interacted with FGFR4. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    CDH2 in vitro9168198 No
    STAT3 in vitro;in vivo11940572,11294897,10918587,12244095,11350938,12626508,8626374,12576423,14551213 CHD related
    FGF7 in vivo7680645 No
    FGF3 in vitro8663044 No
    FGF4 in vitro8663044 CHD related
    FGF5 in vitro8663044 CHD related
    PLCG1 in vitro7518429 CHD related
    FGF9 in vitro8663044 CHD related
    FGF17 in vitro10751172 No
    FGF18 in vitro10751172 No
    EPHA4 in vivo16365308 No
    FGF2 in vitro8530375 CHD related
    FGF6 in vivo1385111 No
    FGFR4 in vitro;in vivo10918587,8576110 CHD related
    STAT1 in vitro;in vivo7657660,11294897,10918587,15322115,7543024,11839738,12817007,7690989,12637327 CHD related
    FGF19 Reconstituted Complex10525310|10525310 No
    FGF1 Reconstituted Complex10736564|10336501 CHD related
    UBC Affinity Capture-Western16091423|17203973 No
    SIRT2 Negative Genetic22318606 No
    FGF8 in vivo10736564 No


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    approvedDB00039PaliferminFor treatment of oral mucositis associated with chemotherapy and radiation therapy.V03AF08